source: branches/alilink/HELP_SOURCE/oldhelp/phyl.hlp

Last change on this file was 6141, checked in by westram, 16 years ago
  • spellchecked all (phew)
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 5.8 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4
5#Please insert subtopic references  (line starts with keyword SUB)
6#SUB    subtopic.hlp
7
8# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
9
10#************* Title of helpfile !! and start of real helpfile ********
11TITLE           Matrices, Masks, Profiles V1.0
12
13OCCURRENCE      ARB_NT/Tree/Dist Matrix V 1.0
14
15DESCRIPTION     This tool allows to calculate distance and similarity matrices
16                for the marked species. Conservation profiles can be established
17                and used as filters for column selection by other programs.
18
19                1. Selection of columns:
20
21                Select part of the alignment to analyze by typing first and last
22                        column numbers after the 'start at column:' and 'stop at
23                        column:' prompts, respectively, and press 'Return' on
24                        the keyboard.
25
26                Select minimum and maximum similarities for the individual
27                        columns to be included for similarity or distance matrix
28                        calculation by typing the values (50 means the most
29                        frequent base at a particular position is shared by at
30                        least 50% of all marked sequences (species)) after the
31                        'minimum similarity:' and 'maximum similarity:' prompts,
32                        respectively, and press 'Return' on the keyboard.
33
34                Define whether alignment gaps and ambiguities within individual
35                        marked sequences (species) should be taken into account:
36
37                        Use the right mouse button to display the submenus
38                        associated to the items below the 'markerline:' prompt
39                        by pressing the respective buttons.
40
41                                don't count:
42                                        Calculate conservation from unambiguous
43                                        bases only
44
45                                don't use column if maximal:
46                                        Exclude column if the respective symbol
47                                        is present in the majority of the marked
48                                        sequences.
49
50                                exclude column:
51                                        Exclude column if the respective symbol
52                                        is present in any of the marked
53                                        sequences.
54
55                                treat as ambiguous:
56                                        Take the respective symbol as an
57                                        unambiguous residue.
58
59                2. After selecting columns define how to treat ambiguities for
60                        distance calculations:
61
62                        Use the right mouse button to display the submenus
63                        associated to the items below the 'distance matrix:'
64                        prompt by pressing the respective buttons.
65
66                                don't count:
67                                        The particular position is not
68                                        included for binary distance
69                                        calculations if the symbol is
70                                        present in one or both sequences.
71
72                                use distance table:
73                                        the symbols are treated as unambiguous
74                                        residues
75
76                3. Calculate profiles and matrices:
77
78                        Use the right mouse button to display the 'CALCULATE'
79                        menu and select 'markerline' (profile) or 'distance
80                        matrix' by releasing the mouse button while the cursor
81                        is positioned on the respective menu button.
82
83                4. Display results:
84
85                        Use the right mouse button to display the 'VIEW'
86                        menu and select 'species', 'markerline' or 'distance
87                        matrix' by releasing the mouse button while the cursor
88                        is positioned on the respective menu button. The names,
89                        the aligment of the marked sequences and the
90                        conservation profile, or the distance matrix are shown
91                        within the display area, respectively.
92
93                        The profile:
94
95                        The fraction of sequences sharing most frequent residue
96                        at a particular alignment position is shown as a number
97                        to read bottom down. Alternatively, the profile can be
98                        displayed as a curve by pressing the <toggle> button in
99                        the left part of the window. It can be smoothed by
100                        selecting a number from the 'smooth' menu (left part of
101                        the window).
102
103                        Editing the aligned sequences and profiles, a name can
104                        be selected by moving the cursor to it and pressing the
105                        left mouse button. Pressing the <reference> button, the
106                        respective sequence is used as a filter superimposed to
107                        profile. This allows to exclude further positions from
108                        subsequent calculations which are not occupied by bases
109                        in the reference.
110
111                        Tha matrix:
112
113                        Editing the matrix, mean values can be calculated for
114                        groups of organisms displayed as triangles (radial tree)
115                        or rectangles (dendrogram) in a tree stored in the
116                        database. The grouping currently or most recently
117                        displayed is used for selecting sequences for the
118                        calculation of mean values. Select a tree by pressing
119                        the <grouping> button in the left area of the window.
120
121                5. Save results:
122
123                        To export distances and profiles (not graphs!!) to
124                        ascii files, use the right mouse button to display the
125                        'SAVE' menu and select the corresponding menu item by
126                        releasing the mouse button while the cursor is
127                        positioned on it.
128
129                                uncoded mline:
130                                        The positional conservation is encoded
131                                        by a sequence of letters: A = 1%,
132                                        B = 5%, ...., Z = 100%.
133
134                                bin mline:
135                                        Included and excluded columns are
136                                        indicated by 1 and 0, respectively.
137
138                                % dif. matrix:
139                                        Dissimilarity values.
140
141                                % sim. matrix:
142                                        Similarity values.
143
144                                phyl/prot distmat:
145                                        Corrected distances according Jukes and
146                                        Cantor (nucleic acid sequences only).
147
148                                pos. vari:
149                                        Number of different residues at the
150                                        particular alignment position.
151
152                6. Reconstruct a tree:
153
154                        Press the <NEIGHBOR> button. The tree is reconstructed
155                        using the neighbour joining method and is stored in the
156                        database as 'tree_neighbour'.
157
158                7. Store profile in the database:
159
160                        Press the <ARBSAVE> button to store any calculated
161                        profile 0 / 1 encoded in the database (SAI). The profile
162                        can be used as filter for other ARB tools.                             
163                         
164NOTES           A new version of the tool is under development.
165
166                It is recommended to calculate profiles here, to save them in
167                the database, and to reconstruct distance matrix trees using
168                'ARB_NT/Tree/Neighbour joining' in combination with the profile
169                as filter.
170
171EXAMPLES        None
172
173WARNINGS        Whenever text is typed to the window, press 'Return' on the
174                keyboard, to ensure that the information is recognized by the
175                program!!!
176
177BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.